I came up with a cheesy idea: what if the curved upper "tailfins" on the Class F Shuttlecraft were designed that way so the shuttle could be assembled in different configurations? (Here's the cheesy part: remember the "extensional boosting units" used in the SPACE: 1999 episode "The Metamorph"?)
Maybe the shuttle craft parts come from a "cold storage" parts bin below hangar. numerous shuttle hulls are stored there in pieces, ready for quick assembly. A typical Connie mission could call for four fully-assembled Class F's at any given time, but the parts bin has many more ready for either repairs of the fully-assembled-four or to assemble more in special circumstances.
Let's say there's a number of different configurations that can be derived from the same set of parts, from travel pods to asteroid prospector scouts to recon party base-camp ships to "fighter" probe-ships. So maybe there's a Class G long-range scout (like in TAS) and also a Class H cargo shuttle. All you have to do is pull the right parts from the bin and assemble them properly; maybe a Class E needs the nacelles attached on top, hence the tailfins.
If memory serves, the TAS long-range scoutship used by Spock, Sulu and Uhura had a rear hatch. Maybe the tailfins provide a handy slot for that type of scoutship to house its impulse engine to make clearance for the hatch.